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X-RAY DIFFRACTION
Materials and Methods page
3WBM
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details 18% (v/v) PEG 5000 MME, 100mM Bis-Tris, 200mM sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 169.89 α = 90
    b = 69.76 β = 96.34
    c = 48.13 γ = 90
     
    Space Group
    Space Group Name:    C 1 2 1
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 95
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 315r
    Collection Date 2012-06-06
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE BL-17A
    Wavelength List 0.9642
    Site PHOTON FACTORY
    Beamline BL-17A
     
     
  •   Refinement Data Hide
    Reflection Details
    Observed Criterion Sigma (F) 0.0
    Observed Criterion Sigma(I) 0.0
    Resolution(High) 2
    Resolution(Low) 47.84
    Number Reflections(All) 37892
    Number Reflections(Observed) 37589
    Percent Possible(Observed) 99.2
    R Merge I(Observed) 0.074
    B(Isotropic) From Wilson Plot 18.85
    Redundancy 3.6
     
    High Resolution Shell Details
    Resolution(High) 2.0
    Resolution(Low) 2.11
    Percent Possible(All) 98.7
    R Merge I(Observed) 0.407
    Mean I Over Sigma(Observed) 3.1
    R-Sym I(Observed) 0.407
    Redundancy 3.6
    Number Unique Reflections(All) 5444
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.0
    Resolution(Low) 43.804
    Cut-off Sigma(F) 1.35
    Number of Reflections(all) 37900
    Number of Reflections(Observed) 37582
    Number of Reflections(R-Free) 1882
    Percent Reflections(Observed) 99.16
    R-Factor(All) 0.2139
    R-Factor(Observed) 0.2139
    R-Work 0.212
    R-Free 0.2486
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Mean Isotropic B Value 40.5243
    Anisotropic B[1][1] -5.2402
    Anisotropic B[1][2] 0.0
    Anisotropic B[1][3] 1.7172
    Anisotropic B[2][2] -0.6102
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 5.8504
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0
    Shell Resolution(Low) 2.0541
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2707
    R-Factor(R-Work) 0.2495
    R-Factor(R-Free) 0.3057
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.0541
    Shell Resolution(Low) 2.1145
    Number of Reflections(R-Free) 140
    Number of Reflections(R-Work) 2736
    R-Factor(R-Work) 0.2273
    R-Factor(R-Free) 0.2893
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1145
    Shell Resolution(Low) 2.1828
    Number of Reflections(R-Free) 137
    Number of Reflections(R-Work) 2725
    R-Factor(R-Work) 0.2221
    R-Factor(R-Free) 0.2637
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.1828
    Shell Resolution(Low) 2.2608
    Number of Reflections(R-Free) 145
    Number of Reflections(R-Work) 2695
    R-Factor(R-Work) 0.2166
    R-Factor(R-Free) 0.2821
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.2608
    Shell Resolution(Low) 2.3513
    Number of Reflections(R-Free) 149
    Number of Reflections(R-Work) 2738
    R-Factor(R-Work) 0.2164
    R-Factor(R-Free) 0.2687
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.3513
    Shell Resolution(Low) 2.4583
    Number of Reflections(R-Free) 135
    Number of Reflections(R-Work) 2724
    R-Factor(R-Work) 0.2341
    R-Factor(R-Free) 0.305
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4583
    Shell Resolution(Low) 2.5879
    Number of Reflections(R-Free) 147
    Number of Reflections(R-Work) 2764
    R-Factor(R-Work) 0.2307
    R-Factor(R-Free) 0.2928
    Percent Reflections(Observed) 99.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.5879
    Shell Resolution(Low) 2.75
    Number of Reflections(R-Free) 128
    Number of Reflections(R-Work) 2764
    R-Factor(R-Work) 0.2355
    R-Factor(R-Free) 0.2567
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.75
    Shell Resolution(Low) 2.9623
    Number of Reflections(R-Free) 150
    Number of Reflections(R-Work) 2747
    R-Factor(R-Work) 0.2311
    R-Factor(R-Free) 0.2816
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.9623
    Shell Resolution(Low) 3.2603
    Number of Reflections(R-Free) 144
    Number of Reflections(R-Work) 2780
    R-Factor(R-Work) 0.22
    R-Factor(R-Free) 0.2619
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.2603
    Shell Resolution(Low) 3.7319
    Number of Reflections(R-Free) 169
    Number of Reflections(R-Work) 2748
    R-Factor(R-Work) 0.2052
    R-Factor(R-Free) 0.239
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 3.7319
    Shell Resolution(Low) 4.7009
    Number of Reflections(R-Free) 131
    Number of Reflections(R-Work) 2802
    R-Factor(R-Work) 0.1779
    R-Factor(R-Free) 0.2047
    Percent Reflections(Observed) 100.0
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 4.7009
    Shell Resolution(Low) 43.8146
    Number of Reflections(R-Free) 163
    Number of Reflections(R-Work) 2770
    R-Factor(R-Work) 0.2092
    R-Factor(R-Free) 0.2231
    Percent Reflections(Observed) 98.0
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    f_plane_restr 0.004
    f_chiral_restr 0.048
    f_dihedral_angle_d 10.792
    f_angle_d 0.672
    f_bond_d 0.003
     
    Coordinate Error
    Luzzati ESD(Observed) 0.23
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2664
    Nucleic Acid Atoms 1050
    Heterogen Atoms 0
    Solvent Atoms 310
     
     
  •   Software and Computing Hide
    Computing
    Data Collection ADSC Quantum
    Data Reduction (intensity integration) MOSFLM
    Data Reduction (data scaling) SCALA
    Structure Solution PHASER
    Structure Refinement PHENIX (phenix.refine: 1.7.3_928)
     
    Software
    refinement PHENIX version: (phenix.refine: 1.7.3_928)
    model building PHASER
    data collection ADSC version: Quantum